Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be ...used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95-100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.
•Thymic differentiation signatures organize leukemia along a developmental track.•The use of differentiation signatures improves upon current classification methods.•Improved disease classification ...may identify therapy-resistant leukemia.
To compare transarterial chemoembolization delivered with drug eluting beads (TACE-DEB) with stereotactioc body radiation therapy (SBRT) in patients with hepatocellular carcinoma (HCC) in a ...multicenter randomized trial.
Patients were included if they were eligible for TACE. They could also be recruited if they required treatment prior to liver transplantation. A maximum of four TACE-DEB procedures and ablation after incomplete TACE-DEB were both allowed. SBRT was delivered in six fractions of 8-9Gy. Primary end point was time to progression (TTP). Secondary endpoints were local control (LC), overall survival (OS), response rate (RR), toxicity, and quality of life (QoL). The calculated sample size was 100 patients.
Between May 2015 and April 2020, 30 patients were randomized to the study. Due to slow accrual the trial was closed prematurely. Two patients in the SBRT arm were considered ineligible leaving 16 patients in the TACE-DEB arm and 12 in the SBRT arm. Median follow-up was 28.1 months. Median TTP was 12 months for TACEDEB and 19 months for SBRT (p=0.15). Median LC was 12 months for TACE-DEB and >40 months (not reached) for SBRT (p=0.075). Median OS was 36.8 months for TACEDEB and 44.1 months for SBRT (p=0.36). A post-hoc analysis showed 100% for SBRT 1- and 2-year LC, and 54.4% and 43.6% for TACE-DEB (p=0.019). Both treatments resulted in RR>80%. Three episodes of possibly related toxicity grade ≥3 were observed after TACE-DEB. No episodes were observed after SBRT. QoL remained stable after both treatment arms.
In this trial, TTP after TACE-DEB was not significantly improved by SBRT, while SBRT showed higher local antitumoral activity than TACE-DEB, without detrimental effects on OS, toxicity and QoL. To overcome poor accrual in randomized trials that include SBRT, and to generate evidence for including SBRT in treatment guidelines, international cooperation is needed.
Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development
1. The biogenesis and maintenance of cilia depend on ...intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme
1, 2. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Biedl syndrome (BBS)
3–5. To uncover new ciliary components, including IFT proteins, we compared
C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the ciliogenic transcription factor, DAF-19
6. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and
bbs genes. Furthermore, we demonstrate that the ciliary structural defect of
C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function.
RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of ...expressed mutations. However, standard approaches for library construction typically require relatively high amounts of input RNA, are labor intensive, and are time consuming. METHODS: Here, we report the outcome of a systematic effort to optimize and streamline steps in strand-specific RNA-seq library construction. RESULTS: This work has resulted in the identification of an optimized messenger RNA isolation protocol, a potent reverse transcriptase for cDNA synthesis, and an efficient chemistry and a simplified formulation of library construction reagents. We also present an optimization of bead-based purification and size selection designed to maximize the recovery of cDNA fragments.
These developments have allowed us to assemble a rapid high throughput pipeline that produces high quality data from amounts of total RNA as low as 25 ng. While the focus of this study is on RNA-seq sample preparation, some of these developments are also relevant to other next-generation sequencing library types.
Despite the frequent co-occurrence of posttraumatic stress disorder and substance use disorder, screening for trauma exposure and posttraumatic stress disorder symptoms is not a routine practice in ...substance use disorder clinics. The aims of this study were to examine the prevalence of exposure to traumatic events, posttraumatic stress disorder symptoms, and subjective sleep quality in substance use disorder inpatients after detoxification. In addition, we analyzed associations of sociodemographics, direct and indirect exposure to traumatic events, and sleep quality with posttraumatic stress disorder symptom severity.
Adults diagnosed with substance use disorder (n = 188; 25% women, mean age 46.6 ± 12.3 years) from 2 inpatient addiction clinics were assessed at approximately 4 days post-admission for age, gender, educational level, self-reported substance use, trauma exposure, general and posttraumatic stress disorder-specific subjective sleep quality, and posttraumatic stress disorder symptom severity. Correlates of posttraumatic stress disorder symptom severity were identified with linear regression analyses.
The prevalence of direct trauma exposure was high (89%), 51% of participants screened positive for posttraumatic stress disorder and 87% reported clinically significant poor sleep quality. Younger age, female gender, direct and indirect exposure to more traumatic events, and poor subjective sleep quality were associated with more severe posttraumatic stress disorder symptoms.
Nearly all substance use disorder patients admitted for detoxification in our study had been directly or indirectly exposed to 1 or more traumatic events, and many reported posttraumatic stress disorder symptoms and poor sleep quality. Younger and female substance use disorder patients were at higher risk of posttraumatic stress disorder symptoms. Our results emphasize the need for systematic screening for direct and indirect trauma exposure, posttraumatic stress disorder symptoms, and poor sleep quality in patients admitted for clinical substance use disorder treatment.
Summary Background Treatment options for recurrent glioblastoma are scarce, with second-line chemotherapy showing only modest activity against the tumour. Despite the absence of well controlled ...trials, bevacizumab is widely used in the treatment of recurrent glioblastoma. Nonetheless, whether the high response rates reported after treatment with this drug translate into an overall survival benefit remains unclear. We report the results of the first randomised controlled phase 2 trial of bevacizumab in recurrent glioblastoma. Methods The BELOB trial was an open-label, three-group, multicentre phase 2 study undertaken in 14 hospitals in the Netherlands. Adult patients (≥18 years of age) with a first recurrence of a glioblastoma after temozolomide chemoradiotherapy were randomly allocated by a web-based program to treatment with oral lomustine 110 mg/m2 once every 6 weeks, intravenous bevacizumab 10 mg/kg once every 2 weeks, or combination treatment with lomustine 110 mg/m2 every 6 weeks and bevacizumab 10 mg/kg every 2 weeks. Randomisation of patients was stratified with a minimisation procedure, in which the stratification factors were centre, Eastern Cooperative Oncology Group performance status, and age. The primary outcome was overall survival at 9 months, analysed by intention to treat. A safety analysis was planned after the first ten patients completed two cycles of 6 weeks in the combination treatment group. This trial is registered with the Nederlands Trial Register ( www.trialregister.nl , number NTR1929). Findings Between Dec 11, 2009, and Nov 10, 2011, 153 patients were enrolled. The preplanned safety analysis was done after eight patients had been treated, because of haematological adverse events (three patients had grade 3 thrombocytopenia and two had grade 4 thrombocytopenia) which reduced bevacizumab dose intensity; the lomustine dose in the combination treatment group was thereafter reduced to 90 mg/m2 . Thus, in addition to the eight patients who were randomly assigned to receive bevacizumab plus lomustine 110 mg/m2 , 51 patients were assigned to receive bevacizumab alone, 47 to receive lomustine alone, and 47 to receive bevacizumab plus lomustine 90 mg/m2 . Of these patients, 50 in the bevacizumab alone group, 46 in the lomustine alone group, and 44 in the bevacizumab and lomustine 90 mg/m2 group were eligible for analyses. 9-month overall survival was 43% (95% CI 29–57) in the lomustine group, 38% (25–51) in the bevacizumab group, 59% (43–72) in the bevacizumab and lomustine 90 mg/m2 group, 87% (39–98) in the bevacizumab and lomustine 110 mg/m2 group, and 63% (49–75) for the combined bevacizumab and lomustine groups. After the reduction in lomustine dose in the combination group, the combined treatment was well tolerated. The most frequent grade 3 or worse toxicities were hypertension (13 26% of 50 patients in the bevacizumab group, three 7% of 46 in the lomustine group, and 11 25% of 44 in the bevacizumab and lomustine 90 mg/m2 group), fatigue (two 4%, four 9%, and eight 18%), and infections (three 6%, two 4%, and five 11%). At the time of this analysis, 144/148 (97%) of patients had died and three (2%) were still on treatment. Interpretation The combination of bevacizumab and lomustine met prespecified criteria for assessment of this treatment in further phase 3 studies. However, the results in the bevacizumab alone group do not justify further studies of this treatment. Funding Roche Nederland and KWF Kankerbestrijding.
Objective This was a systematic review and meta-analysis of the mode of anesthesia and outcome after endovascular aneurysm repair (EVAR). Methods Review methods were according to the Preferred ...Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Published and unpublished literature was searched. The primary outcome was 30-day mortality. Secondary outcomes were categorized for patient selection, perioperative outcomes, and postoperative outcomes. Weighted mean differences (WMD) were calculated for continuous variables, such as length of stay, and pooled odds ratios (OR) were calculated for discrete variables such as major morbidity. Results Ten studies of 13,459 patients given local anesthesia (LA) or general anesthesia (GA) were eligible for analysis. There was no difference in 30-day mortality. The LA patients were older than the GA patients (WMD, 0.17; P = .006), with an increased burden of cardiac (LA vs GA: OR, 1.28; P = .011) and respiratory (LA vs GA: OR, 1.28; P = .006) comorbidity. LA EVAR was reported with shorter operative time (WMD, −0.54; P = .001) and hospital stay (WMD, −0.27; P = .001) vs GA. LA patients developed fewer postoperative complications than GA patients (OR, 0.54; P < .001). Conclusions The absence of randomized data is a major hurdle to understanding the effect of anesthetic technique on morbidity after EVAR. The data presented are encouraging in selected patients. The use of locoregional anesthesia for EVAR should be further investigated with better reporting of aneurysm morphology to clarify its potential benefits and identify the subgroups that will derive greatest benefit.
Feature selection (FS) process is essential in the medical area as it reduces the effort and time needed for physicians to measure unnecessary features. Choosing useful variables is a difficult task ...with the presence of censoring which is the unique characteristic in survival analysis. Most survival FS methods depend on Cox's proportional hazard model; however, machine learning techniques (MLT) are preferred but not commonly used due to censoring. Techniques that have been proposed to adopt MLT to perform FS with survival data cannot be used with the high level of censoring. The researcher's previous publications proposed a technique to deal with the high level of censoring. It also used existing FS techniques to reduce dataset dimension. However, in this paper a new FS technique was proposed and combined with feature transformation and the proposed uncensoring approaches to select a reduced set of features and produce a stable predictive model.
In this paper, a FS technique based on artificial neural network (ANN) MLT is proposed to deal with highly censored Endovascular Aortic Repair (EVAR). Survival data EVAR datasets were collected during 2004 to 2010 from two vascular centers in order to produce a final stable model. They contain almost 91% of censored patients. The proposed approach used a wrapper FS method with ANN to select a reduced subset of features that predict the risk of EVAR re-intervention after 5 years to patients from two different centers located in the United Kingdom, to allow it to be potentially applied to cross-centers predictions. The proposed model is compared with the two popular FS techniques; Akaike and Bayesian information criteria (AIC, BIC) that are used with Cox's model.
The final model outperforms other methods in distinguishing the high and low risk groups; as they both have concordance index and estimated AUC better than the Cox's model based on AIC, BIC, Lasso, and SCAD approaches. These models have p-values lower than 0.05, meaning that patients with different risk groups can be separated significantly and those who would need re-intervention can be correctly predicted.
The proposed approach will save time and effort made by physicians to collect unnecessary variables. The final reduced model was able to predict the long-term risk of aortic complications after EVAR. This predictive model can help clinicians decide patients' future observation plan.
The Genome Project–Write Boeke, Jef D.; Church, George; Hessel, Andrew ...
Science (American Association for the Advancement of Science),
07/2016, Letnik:
353, Številka:
6295
Journal Article
Recenzirano
The Human Genome Project ("HGP-read"), nominally completed in 2004, aimed to sequence the human genome and to improve the technology, cost, and quality of DNA sequencing (1, 2). It was biology's ...first genome-scale project and at the time was considered controversial by some. Now, it is recognized as one of the great feats of exploration, one that has revolutionized science and medicine.
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